The identification of related polypeptides has been accomplished mainly through methods of nucleic acid hybridization. Although a powerful tool that has resulted in the identification and characterization of many protein families, nucleic acid hybridization is limited by the requirement that structural similarity exist between the probe nucleic acid and the target nucleic acid. While conditions may be adjusted to vary the amount of similarity needed before hybridization occurs, a certain threshold sequence homology is needed for meaningful identification. When the degree of similarity falls below this threshold, identified polypeptides are less likely to truly be related in structure, evolution, and function. Moreover, even proteins that may be significantly related in structure may be overlooked if the nucleic acid probe happens to be from a region of low homology.
By way of contrast, using functional similarity as the key to relate families of polypeptides obviates concerns about both false positive and false negative identification. While the level of function may vary, a polypeptide either possesses the function of interest or it does not. And the presence of a given function demonstrates that a protein is significantly related to other proteins expressing a similar function, regardless of structure. A strategy for the identification of related proteins that uses the presence of a certain function as the selection criteria would constitute a significant advance over the prior art methods of hybridization identification.
Phosphorylation of tyrosine residues in proteins plays a critical role in fundamental cell functions. Hanks et al., Science 241:42-52 (1988); Ullrich and Schlessinger, Cell 61:203-212 (1990); Aaronson, Science 254:1146phosphorylation is often transient, being regulated within the cell by protein tyrosine kinases ("PTK's") and protein tyrosine phosphatases ("PTP's"). Fischer et al., Science 253:401-406 (1991); Hunter, Cell 58:1013-1016 (1989). Recently, attention has been directed to the PTP family which, like PTK's, has been implicated in cell signalling, cell growth and proliferation, and oncogenic transformation. Moreover, recent discoveries have shown that some PTP's can be involved in cell-cycle regulation and embryogenesis. Kumagai and Dunphy, Cell 64:903-914 (1991); Gould and Nurse, Nature 342:39-45 (1989); Dunphy and Newport, Cell 58:181-191 (1989); Yang et al., Cell 67:661-673 (1991); Tian et al., Cell 67:675-685 (1991). Because of these attributes, abnormalities in PTP's are considered as potential causes of cancer and other diseases.
Members of the PTP family have, heretofore, been identified by laborious protein purification protocols and genetic complementation in yeast. Fischer et al. (1991); Lau and Nathans, Proc. Nat'l Acad. Sci. U.S.A. 84:1182-1186 (1987). However, the great majority have been identified on the basis of similarities in nucleic acid sequence. To date, these proteins have been observed to share a sequence similarity in their catalytic domains. Charbonneau et al., Proc. Nat'l Acad. Sci. U.S.A. 86:5252-5256 (1989); Krueger et al., EMBO J. 9:3241-3251 (1990). Due to limitations that apply to identification of PTP's by structural homology, however, it is possible that other PTP's, having significantly less structural homology, have been overlooked.